Jitter is definitely the great bugaboo of many transports. When I was putting together my first new system in 15 years, I opted for a DVD player/external DAC combination thinking that the external DAC would provide all of the performance improvement I needed. I was greatly disappointed in the performance and didn't know where to look for ways to improve matters. I borrowed a dbx Quantum mastering processor to experiment with EQ and to my great surprise, without any EQ at all, the sound was better than I'd ever heard. The difference was the reclocking that was done and the subsequent reduction in jitter. Since I couldn't afford a Quantum, I searched for another solution and found a device called the Tent X3. It's a reclocking circuit that you can add to some standard CD players that replaces the original system clock, then refines the edges of the S/PDIF signal that it generates. The results are remarkable. I took a Marantz CD67(?) player which was horrible as a transport and turned it into an amazing transport with the addition of this device. I would suspect that very high end transports do all kinds of things to reduce jitter.
As far as cables go, I think a bad cable can mess up a good transport but I've never heard a good cable compensating for a bad transport.